The Payment for Ecosystem Services (PES) is an economic tool that has emerged in recent years as a mechanism to promote conservation of natural resources, as well as that of various goods and services commonly used. However, its application in practice raises a number of ethical concerns that this study seeks to discuss. The concept and benefits of PES are discussed, emphasizing its neoclassical economic nature background and how the initial anthropogenic position has evolved into a more holistic ecosystem vision. The paper examines some of the relationships between ethics and ecosystem services as well as the natural conflicts emerging from the opposition of utilitarian economic values versus moral arguments and deontological ethical systems. Then, a justification for ethics in payment for ecosystem services is provided as an attempt to solve perceived conflicts between conservation and human welfare. Later, the right to benefit from natural resources and PES is discussed. The conflict between natural resources as public goods whose use is a universal right for all human beings and the property rights, either legal or ancestral, of indigenous and originary people is stressed. Finally, the future of ethics and ecosystem services on issues such as the well-being of future generations and the search of an efficient integration based on land planning and conservation management strategies is discussed. In conclusion, the paper emphasizes the need for a better, integrated accounting of the benefits and costs of nature conservation, which will probably only occur when teams of natural and social scientists work together.